Genomics

  • Article
    | Open Access

    A large-scale metagenomic analysis of plant and mammal environmental DNA reveals complex ecological changes across the circumpolar region over the past 50,000 years, as biota responded to changing climates, culminating in the postglacial extinction of large mammals and emergence of modern ecosystems.

    • Yucheng Wang
    • , Mikkel Winther Pedersen
    •  & Eske Willerslev
  • Article |

    Whole-genome sequencing analysis of somatic mutations in liver samples from patients with chronic liver disease identifies driver mutations in metabolism-related genes such as FOXO1, and shows that these variants frequently exhibit convergent evolution.

    • Stanley W. K. Ng
    • , Foad J. Rouhani
    •  & Peter J. Campbell
  • Article
    | Open Access

    A comprehensive survey of the epigenome from 45 regions of the mouse cortex, hippocampus, striatum, pallidum and olfactory areas using single-nucleus DNA methylation sequencing enables identification of 161 cell clusters with distinct locations and projection targets and provides insights into the regulatory landscape underlying neuronal diversity and spatial regulation.

    • Hanqing Liu
    • , Jingtian Zhou
    •  & Joseph R. Ecker
  • Article |

    Whole-genome sequencing of haematopoietic colonies from human fetuses reveals the somatic mutations acquired by individual progenitors, which are used as barcodes to construct a phylogenetic tree of blood development.

    • Michael Spencer Chapman
    • , Anna Maria Ranzoni
    •  & Ana Cvejic
  • Article
    | Open Access

    A revised, universal nomenclature for the vertebrate genes that encode the oxytocin and vasopressin–vasotocin ligands and receptors will improve our understanding of gene evolution and facilitate the translation of findings across species.

    • Constantina Theofanopoulou
    • , Gregory Gedman
    •  & Erich D. Jarvis
  • Article |

    NanoSeq is used to detect mutations in single DNA molecules and analyses show that mutational processes that are independent of cell division are important contributors to somatic mutagenesis.

    • Federico Abascal
    • , Luke M. R. Harvey
    •  & Iñigo Martincorena
  • Article
    | Open Access

    The complete assembly of human chromosome 8 resolves previous gaps and reveals hidden complex forms of genetic variation, enabling functional and evolutionary characterization of primate centromeres.

    • Glennis A. Logsdon
    • , Mitchell R. Vollger
    •  & Evan E. Eichler
  • Article |

    Single-cell analysis of genomes from primary human breast tumours and cell lines shows that chromosomal aberrations continue to evolve during primary tumour expansion, resulting in a milieu of subclones within the tumour.

    • Darlan C. Minussi
    • , Michael D. Nicholson
    •  & Nicholas E. Navin
  • Article |

    Phylogenies of human placental cells based on whole-genome sequencing of bulk samples and microdissections reveal extensive mutagenesis in placental tissue, and suggest that mosaicism is a typical part of normal placental development.

    • Tim H. H. Coorens
    • , Thomas R. W. Oliver
    •  & Sam Behjati
  • Article |

    Siberian mammoth genomes from the Early and Middle Pleistocene subepochs reveal adaptive changes and a key hybridization event, highlighting the value of deep-time palaeogenomics for studies of speciation and long-term evolutionary trends.

    • Tom van der Valk
    • , Patrícia Pečnerová
    •  & Love Dalén
  • Article
    | Open Access

    The genome of the biofuel crop switchgrass (Panicum virgatum) reveals climate–gene–biomass associations that underlie adaptation in nature and will facilitate improvements of the yield of this crop for bioenergy production.

    • John T. Lovell
    • , Alice H. MacQueen
    •  & Jeremy Schmutz
  • Article
    | Open Access

    A chromosome-quality genome of the lungfish Neoceratodus fosteri sheds light on the development of obligate air-breathing and the gain of limb-like gene expression in lobed fins, providing insights into the water-to-land transition in vertebrate evolution.

    • Axel Meyer
    • , Siegfried Schloissnig
    •  & Manfred Schartl
  • Article
    | Open Access

    New reference genomes of the two extant monotreme lineages (platypus and echidna) reveal the ancestral and lineage-specific genomic changes that shape both monotreme and mammalian evolution.

    • Yang Zhou
    • , Linda Shearwin-Whyatt
    •  & Guojie Zhang
  • Article |

    Ancient DNA reveals genetic differences between stone-tool users and people associated with ceramic technology in the Caribbean and provides substantially lower estimates of population sizes in the region before European contact.

    • Daniel M. Fernandes
    • , Kendra A. Sirak
    •  & David Reich
  • Article |

    A high-throughput, chromosome-wide analysis of DNA looping reveals its contribution to the organization of chromatin, and provides insight into how nucleosomes are deposited and organised de novo.

    • Aakash Basu
    • , Dmitriy G. Bobrovnikov
    •  & Taekjip Ha
  • Article
    | Open Access

    Chromosome-scale sequence assemblies of 20 diverse varieties of barley are used to construct a first-generation pan-genome, revealing previously hidden genetic variation that can be used by studies aimed at crop improvement

    • Murukarthick Jayakodi
    • , Sudharsan Padmarasu
    •  & Nils Stein
  • Article
    | Open Access

    Comparison of multiple genome assemblies from wheat reveals extensive diversity that results from the complex breeding history of wheat and provides a basis for further potential improvements to this important food crop.

    • Sean Walkowiak
    • , Liangliang Gao
    •  & Curtis J. Pozniak
  • Article |

    A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.

    • Shaohong Feng
    • , Josefin Stiller
    •  & Guojie Zhang
  • Analysis
    | Open Access

    A whole-genome alignment of 240 phylogenetically diverse species of eutherian mammal—including 131 previously uncharacterized species—from the Zoonomia Project provides data that support biological discovery, medical research and conservation.

    • Diane P. Genereux
    • , Aitor Serres
    •  & Elinor K. Karlsson
  • Article |

    Analysis of cis-regulatory chromatin interactions, open chromatin and transcriptomes for different cell types isolated from mid-gestational human cortex samples provides insights into gene regulation during development.

    • Michael Song
    • , Mark-Phillip Pebworth
    •  & Yin Shen
  • Article |

    A combination of clonal expansion and DNA amplification is used to sequence genetic material from individual melanocytes, shedding light on the mutational landscape of these cells and the development of melanomas.

    • Jessica Tang
    • , Eleanor Fewings
    •  & A. Hunter Shain
  • Article
    | Open Access

    The approximately 5-Gb tuatara (Sphenodon punctatus) genome assembly provides a resource for analysing amniote evolution, and highlights the imperative for meaningful cultural engagement with Indigenous communities in genome-sequencing endeavours.

    • Neil J. Gemmell
    • , Kim Rutherford
    •  & Haydn Edmonds
  • Article
    | Open Access

    ChIP–seq and CETCh–seq data are used to analyse binding maps for 208 transcription factors and other chromatin-associated proteins in a single human cell type, providing a comprehensive catalogue of the transcription factor landscape and gene regulatory networks in these cells.

    • E. Christopher Partridge
    • , Surya B. Chhetri
    •  & Eric M. Mendenhall
  • Article |

    Genome-wide analysis of tandem DNA repeats in the genomes of individuals with autism spectrum disorder and control participants reveals a strong contribution of tandem repeat expansions to the genetic aetiology and phenotypic complexity of autism spectrum disorder.

    • Brett Trost
    • , Worrawat Engchuan
    •  & Ryan K. C. Yuen
  • Article
    | Open Access

    Reference-quality genomes for six bat species shed light on the phylogenetic position of Chiroptera, and provide insight into the genetic underpinnings of the unique adaptations of this clade.

    • David Jebb
    • , Zixia Huang
    •  & Emma C. Teeling
  • Article
    | Open Access

    High-coverage, ultra-long-read nanopore sequencing is used to create a new human genome assembly that improves on the coverage and accuracy of the current reference (GRCh38) and includes the gap-free, telomere-to-telomere sequence of the X chromosome.

    • Karen H. Miga
    • , Sergey Koren
    •  & Adam M. Phillippy
  • Article |

    Genomic analyses of DNA from modern individuals show that, about 800 years ago, pre-European contact occurred between Polynesian individuals and Native American individuals from near present-day Colombia, while remote Pacific islands were still being settled.

    • Alexander G. Ioannidis
    • , Javier Blanco-Portillo
    •  & Andrés Moreno-Estrada
  • Article |

    Resequencing analyses of three species of wild sunflower identify large non-recombining haplotype blocks that correlate with ecologically relevant traits, soil and climate characteristics, and that differentiate species ecotypes.

    • Marco Todesco
    • , Gregory L. Owens
    •  & Loren H. Rieseberg
  • Article |

    Skeletal remains from the Neolithic passage tomb at Newgrange (Ireland) represent the adult son of a first-degree incestuous union, suggesting that a politico-religious elite may have controlled the construction of Irish sites of this type.

    • Lara M. Cassidy
    • , Ros Ó Maoldúin
    •  & Daniel G. Bradley
  • Article |

    Thousands of sperm genomes have been analysed with a new method called Sperm-seq, revealing interconnected meiotic variation at the single-cell and person-to-person levels, and suggesting chromosome compaction as a way to explain the relationships between diverse recombination phenotypes.

    • Avery Davis Bell
    • , Curtis J. Mello
    •  & Steven A. McCarroll